Homeworlds being controlled by Darkness is supposed to be for the benefit of new players as they shouldnt immediately get arrested when they walk out of the front door after spawning.

It also allows the admins to be able to rejig the planet to be able to provide 'essential' basic services as the need arises during the games development cycles. As such all(mostly) homeworlds have as a minimum a shop and NPC transport.

GE still controls a few but their policy is to unmolest new players if they are found in the spawn city. Regardless to their affiliation. That doesn't extend to them traveling outside of that city, nor giving shield access for pickup. After all, they can use the NPC transports or spawn a ship to get off the planets.

Guess it should be unmolested: not interfered with, disturbed, or harmed.

The old homeworld tend to be owned. Most of those are important planets in canon. Some of those could be Darkness controlled? Possibly? But you can't really imagine Coruscant to not be controlled by the GE. Likewise other planets may not seem right being Darkness owned. The NR uses Kashyyyk as a rallying point. And of course FF would not be the same if Falleen wasn't controlled by them.

Can I expand the question to quench my curiosity?
If someone discovers a hidden system that is a home world, do they loose the right to Darkness to control the planet? It would seem pretty harsh if someone had been scouting to find a hidden system :/

Yes. The homeworlds in hidden systems are already Darkness controlled so upon finding it that planet will be effectively locked out. However there are usually/occasionally other planets in the system to claim.